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‎.github/workflows/R-CMD-check.yaml‎

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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches: [main, master]
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pull_request:
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branches: [main, master]
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workflow_dispatch:
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name: 'R CMD check'
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permissions: read-all
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jobs:
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R-CMD-check:
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timeout-minutes: 10
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runs-on: ${{ matrix.config.os }}
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name: ${{ matrix.config.os }} (${{ matrix.config.r }})
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strategy:
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fail-fast: true
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matrix:
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config:
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- {os: macos-latest, r: 'release'}
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- {os: windows-latest, r: 'release'}
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# - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
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- {os: ubuntu-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'oldrel-1'}
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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R_KEEP_PKG_SOURCE: yes
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steps:
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/setup-r@v2
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with:
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r-version: ${{ matrix.config.r }}
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http-user-agent: ${{ matrix.config.http-user-agent }}
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use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::rcmdcheck
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needs: check
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- uses: r-lib/actions/check-r-package@v2
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with:
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upload-snapshots: true
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build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
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# # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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# on:
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# push:
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# branches: [main, master]
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# pull_request:
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# branches: [main, master]
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# workflow_dispatch:
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# name: 'R CMD check'
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# permissions: read-all
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# jobs:
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# R-CMD-check:
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# timeout-minutes: 10
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# runs-on: ${{ matrix.config.os }}
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# name: ${{ matrix.config.os }} (${{ matrix.config.r }})
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# strategy:
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# fail-fast: true
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# matrix:
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# config:
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# - {os: macos-latest, r: 'release'}
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# - {os: windows-latest, r: 'release'}
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# # - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
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# - {os: ubuntu-latest, r: 'release'}
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# - {os: ubuntu-latest, r: 'oldrel-1'}
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# env:
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# GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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# R_KEEP_PKG_SOURCE: yes
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# steps:
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# - uses: actions/checkout@v4
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# - uses: r-lib/actions/setup-pandoc@v2
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# - uses: r-lib/actions/setup-r@v2
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# with:
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# r-version: ${{ matrix.config.r }}
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# http-user-agent: ${{ matrix.config.http-user-agent }}
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# use-public-rspm: true
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# - uses: r-lib/actions/setup-r-dependencies@v2
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# with:
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# extra-packages: any::rcmdcheck
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# needs: check
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# - uses: r-lib/actions/check-r-package@v2
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# with:
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# upload-snapshots: true
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# build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

‎.github/workflows/pkgdown.yaml‎

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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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# push:
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# branches: [main, master]
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# pull_request:
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# branches: [main, master]
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# release:
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# types: [published]
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workflow_dispatch:
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# # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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# on:
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# # push:
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# # branches: [main, master]
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# # pull_request:
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# # branches: [main, master]
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# # release:
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# # types: [published]
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# workflow_dispatch:
1111

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name: 'pkgdown Quarto manuscript'
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# name: 'pkgdown Quarto manuscript'
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permissions: read-all
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# permissions: read-all
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jobs:
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pkgdown:
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timeout-minutes: 10
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runs-on: macos-latest
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# Only restrict concurrency for non-PR jobs
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concurrency:
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group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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permissions:
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contents: write
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steps:
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- uses: actions/checkout@v4
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# jobs:
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# pkgdown:
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# timeout-minutes: 10
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# runs-on: macos-latest
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# # Only restrict concurrency for non-PR jobs
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# concurrency:
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# group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
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# env:
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# GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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# permissions:
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# contents: write
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# steps:
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# - uses: actions/checkout@v4
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- name: Set up Quarto
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uses: quarto-dev/quarto-actions/setup@v2
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# - name: Set up Quarto
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# uses: quarto-dev/quarto-actions/setup@v2
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- uses: r-lib/actions/setup-pandoc@v2
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# - uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/setup-tinytex@v2
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- run: tlmgr --version
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# - uses: r-lib/actions/setup-tinytex@v2
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# - run: tlmgr --version
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- uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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# - uses: r-lib/actions/setup-r@v2
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# with:
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# use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: |
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any::pkgdown
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local::.
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any::tidyverse
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any::gt
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any::here
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any::flextable
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any::ggh4x
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any::pkgdepR
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any::semPlot
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any::semptools
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any::magick
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any::pdftools
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any::cowplot
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any::tictoc
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any::mvtnorm
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any::katex
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any::ggExtra
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needs: website
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# - uses: r-lib/actions/setup-r-dependencies@v2
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# with:
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# extra-packages: |
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# any::pkgdown
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# local::.
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# any::tidyverse
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# any::gt
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# any::here
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# any::flextable
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# any::ggh4x
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# any::pkgdepR
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# any::semPlot
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# any::semptools
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# any::magick
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# any::pdftools
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# any::cowplot
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# any::tictoc
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# any::mvtnorm
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# any::katex
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# any::ggExtra
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# needs: website
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- name: Build site
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run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
66-
shell: Rscript {0}
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# - name: Build site
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# run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
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# shell: Rscript {0}
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- name: Render brsem manuscript
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uses: quarto-dev/quarto-actions/render@v2
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with:
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path: manuscript/brsem/
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# - name: Render brsem manuscript
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# uses: quarto-dev/quarto-actions/render@v2
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# with:
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# path: manuscript/brsem/
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- name: Render plugin manuscript
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uses: quarto-dev/quarto-actions/render@v2
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with:
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path: manuscript/plugin
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# - name: Render plugin manuscript
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# uses: quarto-dev/quarto-actions/render@v2
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# with:
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# path: manuscript/plugin
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- name: Deploy to GitHub pages 🚀
79-
if: github.event_name != 'pull_request'
80-
uses: JamesIves/github-pages-deploy-action@v4.5.0
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with:
82-
clean: false
83-
branch: gh-pages
84-
folder: docs
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# - name: Deploy to GitHub pages 🚀
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# if: github.event_name != 'pull_request'
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# uses: JamesIves/github-pages-deploy-action@v4.5.0
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# with:
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# clean: false
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# branch: gh-pages
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# folder: docs

‎.github/workflows/test-coverage.yaml‎

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@@ -1,63 +1,63 @@
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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
3-
on:
4-
push:
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branches: [main, master]
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pull_request:
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branches: [main, master]
8-
workflow_dispatch:
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name: 'Code coverage'
11-
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permissions: read-all
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jobs:
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test-coverage:
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timeout-minutes: 5
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runs-on: ubuntu-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
20-
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steps:
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- uses: actions/checkout@v4
23-
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- uses: r-lib/actions/setup-r@v2
25-
with:
26-
use-public-rspm: true
27-
28-
- uses: r-lib/actions/setup-r-dependencies@v2
29-
with:
30-
extra-packages: any::covr, any::xml2
31-
needs: coverage
32-
33-
- name: Test coverage
34-
run: |
35-
cov <- covr::package_coverage(
36-
quiet = FALSE,
37-
clean = FALSE,
38-
install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
39-
)
40-
covr::to_cobertura(cov)
41-
shell: Rscript {0}
42-
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- uses: codecov/codecov-action@v4
44-
with:
45-
fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
46-
file: ./cobertura.xml
47-
plugin: noop
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disable_search: true
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token: ${{ secrets.CODECOV_TOKEN }}
50-
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- name: Show testthat output
52-
if: always()
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run: |
54-
## --------------------------------------------------------------------
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find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
56-
shell: bash
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- name: Upload test results
59-
if: failure()
60-
uses: actions/upload-artifact@v4
61-
with:
62-
name: coverage-test-failures
63-
path: ${{ runner.temp }}/package
1+
# # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
2+
# # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
3+
# on:
4+
# push:
5+
# branches: [main, master]
6+
# pull_request:
7+
# branches: [main, master]
8+
# workflow_dispatch:
9+
10+
# name: 'Code coverage'
11+
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# permissions: read-all
13+
14+
# jobs:
15+
# test-coverage:
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# timeout-minutes: 5
17+
# runs-on: ubuntu-latest
18+
# env:
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# GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
20+
21+
# steps:
22+
# - uses: actions/checkout@v4
23+
24+
# - uses: r-lib/actions/setup-r@v2
25+
# with:
26+
# use-public-rspm: true
27+
28+
# - uses: r-lib/actions/setup-r-dependencies@v2
29+
# with:
30+
# extra-packages: any::covr, any::xml2
31+
# needs: coverage
32+
33+
# - name: Test coverage
34+
# run: |
35+
# cov <- covr::package_coverage(
36+
# quiet = FALSE,
37+
# clean = FALSE,
38+
# install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
39+
# )
40+
# covr::to_cobertura(cov)
41+
# shell: Rscript {0}
42+
43+
# - uses: codecov/codecov-action@v4
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# with:
45+
# fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
46+
# file: ./cobertura.xml
47+
# plugin: noop
48+
# disable_search: true
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# token: ${{ secrets.CODECOV_TOKEN }}
50+
51+
# - name: Show testthat output
52+
# if: always()
53+
# run: |
54+
# ## --------------------------------------------------------------------
55+
# find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
56+
# shell: bash
57+
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# - name: Upload test results
59+
# if: failure()
60+
# uses: actions/upload-artifact@v4
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# with:
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# name: coverage-test-failures
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# path: ${{ runner.temp }}/package

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